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Table 1 Results from the analyses of positive selection (PAML v 4.7, Yang 2007)

From: Selective forces acting during multi-domain protein evolution: the case of multi-domain globins

Model

lnL

κ

np

Model estimates

LRT (df)

Sites under positive selection (BEB >0.95)

Branchipolynoe

 Branch model

  M0

−2,061.60

1.755

19

ω = 0.278

  

  M1

−2,052.07

1.781

35

0.001 < ω < ∞

19.05NS (16)

 

 Site model

  M1a ‘nearly neutral’

−2,050.01

1.842

20

ω0 = 0.177 (79%)

ω1 = 1.000 (21%)

  

  M2a ‘positive selection’

−2,050.01

1.842

22

ω0 = 0.177 (79%)

ω1 = 1.000 (10.8%)

ω2 = 1.000 (10.2%)

0.00NS (2)

 

 Branch-site model

  MA branch a (duplication)

−2,038.08

1.851

22

ω0 = 0.154 (65.6%)

ω1 = 1.000 (16.3%)

ω2a = ∞ (14.5%)

ω2b = ∞ (3.6%)

23.86***** (2)

27 V

30A

52Q

65C

  MA branch b (D4 vs D3 D2 D1)

−2,049.37

1.845

22

ω0 = 0.167 (0%)

ω1 = 1.000 (0%)

ω2a = 1.076 (78.5%)

ω2b = 1.076 (21.5%)

1.29NS

–

  MA_branch c (D2 D1)

−2,048.87

1.856

22

ω0 = 0.167 (0%)

ω1 = 1.000 (0%)

ω2a = 2.6 (79.6%)

ω2b = 2.6 (20.4%)

2.28NS

–

Nematodes

 Branch model

  M0

−2,153.41

1.455

9

ω = 0.037

  

  M1

−2146.71

1.313

15

0.029 < ω < ∞

13.4* (6)

 

 Site model

  M1a ‘nearly neutral’

−2,141.70

1.476

10

ω0 = 0.071 (87.3%)

ω1 = 1.000 (12.7%)

  

  M2a ‘positive selection’

−2,141.70

1.476

12

ω0 = 0.071 (87.3%)

ω1 = 1.000 (3.0%)

ω2 = 1.000 (9.7%)

0NS

 

 Branch-site model

  MA branch a (duplication)

−2,133.19

1.565

12

ω0 = 0.074 (51.2%)

ω1 = 1.000 (7.2%)

ω2a = 1.412 (36.4%)

ω2b = 1.412 (5.2%)

17.02***** (2)

MA vs MAω=1 NS

16 sites

  MA branch b (D1)

−2,135.16

1.407

12

ω0 = 0.063 (74.2%)

ω1 = 1.000 (10.2%)

ω2a = ∞ (13.7%)

ω2b = ∞ (1.9%)

13.09**** (2)

11A

  MA branch c (D2)

−2,128.13

1.373

12

ω0 = 0.061 (79.1%)

ω1 = 1.000 (9.5%)

ω2a = ∞ (10.2%)

ω2b = ∞ (1.2%)

27.14***** (2)

–

Barbatia

 Branch model

  M0

−1,989.05

1.398

11

ω = 0.332

  

  M1

−1,980.29

1.393

19

0.136 < ω < 3.160

17.54** (8)

 

 Site model

  M1a

−1,967.14

1.514

12

ω0 = 0.128 (62%)

ω1 = 1.000 (34%)

  

  M2a

−1,956.20

1.649

14

ω0 = 0.120 (54.9%)

ω1 = 1.000 (43.1%)

ω2 = ∞ (2%)

21.88***** (2)

 

 Branch-site model

  MA branch a (duplication)

−1,961.52

1.572

14

ω0 = 0.119 (59.9%)

ω1 = 1.000 (29.5%)

ω2a = ∞ (7.1%)

ω2b = ∞ (3.5%)

11.24*** (2)

–

  MA branch b (D1)

−1,962.64

1.510

14

ω0 = 0.117 (62.3%)

ω1 = 1.000 (31.5%)

ω2a = ∞ (4.1%)

ω2b = ∞ (2.1%)

9.00** (2)

31G

  1. In the 4 invertebrate groups, the likelihood (ln) values correspond to branches leading to various duplications (see Fig. 1a–c) in each phylogram. Selection models implemented in the codeml package, its parameters and associated results of likelihood ratio tests (LRT) are shown (significance threshold: p < 0.05).
  2. κ transition/transversion ratio, np number of parameters estimated by the model, model estimates: ω 0  estimated ω for the category of sites under purifying selection (ω < 1), ω 1 estimated ω for sites for the category under neutral evolution (ω ~ 1), ω 2a estimated ω for sites under positive selection in the foreground branches against background branches under purifying selection, ω 2b  estimated ω for sites under positive selection in the foreground branches against background branches under neutral evolution, df degrees of freedom, NS non significant.
  3. * Significant at 0.05; ** significant at 0.025; *** significant at 0.01; **** significant at 0.005; ***** significant at 0.001; BEB >0.95: sites identified by Bayes Empirical Bayes analysis with a posterior probability greater than 95%.
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